I'm interested in quantitative analysis of a gene and it's corresponding protein known to have a crucial role in a bacteria. As much as I understand, we can do quantitative analysis using transcriptomic data (RNA-Seq) and get a list of genes involved in particular disease or organism. I don't understand how we can quantify single gene and it's corresponding protein using bioinformatics approach? As opposed to western blot or immunohistology used for experimental approach. Please help I have to address a reviewer's comment soon.
<sarcasm> We better jump on this since you have to address the comments soon. </sarcasm>
If by bioinformatics approach you mean something purely predictive without any experiments, I don't think there is a way to do that in general. There are some genes that are part of well-studied operons (say, RNA polymerase subunits inside ribosomal operons) that can be predicted as highly expressed simply because they are next to genes that are known to be highly expressed. In general, however, a quantitative analysis requires experiments.
Keeping that in mind, you have already answered your own question. RNAseq will tell us about differences in mRNA levels between a baseline condition and some other condition that is of interest to us. Generally speaking, genes will be unchanged, up- or down-regulated compared to the baseline condition, and you pull out your gene of interest from the whole list. The same is true for quantification at protein level, except that now we extract proteins, run them on a 2D gel, and quantify the difference by mass-spec.
Neither RNAseq nor proteomics are purely bioinformatics approaches, but their interpretation relies heavily on bioinformatics in final stages.
